Title I: Railroad Safety Improvements - (Sec. 101) Requires the Federal Railroad Administration (FRA) to: (1) make safety in railroad transportation the highest priority in carrying out its duties; and (2) have a Deputy Administrator and an Associate Administrator for Railroad Safety, who shall be the FRA's Chief Safety Officer.

(Sec. 102) Directs the Secretary of Transportation (Secretary) to: (1) develop a long-term railroad strategy for improving railroad safety to cover at least five years; and (2) report annually to Congress on the FRA's performance in achieving its strategic goals and annual plans.

(Sec. 103) Directs the Secretary to require each Class I railroad carrier, a railroad carrier that has inadequate safety performance, or a railroad that provides intercity passenger or commuter rail passenger transportation to develop, submit for Secretary approval, and if approved implement a railroad safety risk reduction program, including risk mitigation, technology implementation, and fatigue management plans, to reduce the rate of railroad accidents and injuries.

Requires the Secretary to ensure that railroad carriers required to submit a technology implementation plan with a schedule for implementing a positive train control system comply with that schedule and implement such system by December 31, 2018.

(Sec. 104) Requires each Class I railroad carrier and each entity providing intercity or commuter rail passenger transportation to develop and submit for Secretary approval a plan for implementing a positive train control system by December 31, 2015.

Grants the Secretary authority to assess civil penalties for violation of related requirements.

(Sec. 105) Directs the Secretary to establish a grant program for the deployment of certain train control and other railroad safety technologies, with priority to projects that focus on making technologies interoperable between railroad systems, accelerate train control technology deployment on high-risk corridors, or benefit both passenger and freight safety and efficiency. Authorizes appropriations for FY2009-FY2013.

(Sec. 106) Directs the Secretary to report annually to Congress on the specific actions taken to implement unmet statutory railroad safety mandates and each open railroad safety recommendation made by the National Transportation Safety Board (NTSB) or the Department of Transportation (DOT) Inspector General.

(Sec. 107) Declares that no railroad safety rule or order issued by the Secretary shall be effective if it incorporates by reference a code, rule, standard, requirement, or practice issued by a nonfederal association or other entity, unless the date on which the code, rule, standard, requirement, or practice was adopted is specifically cited in the rule or order, or the code, rule, standard, requirement, or practice has been subject to notice and comment under a federal railroad safety rule or order.

(Sec. 108) Revises the definition of a signal employee to eliminate the requirement that he or she be employed by a railroad carrier (thus including signal employees employed by contractors or subcontractors).

Revises hours of service requirements for a train employee. Prohibits a railroad carrier, and its officers and agents, from requiring a train employee to remain or go on duty or be in any other mandatory service: (1) where the employee has spent in any calendar month a total of 276 hours on duty, or waiting for deadhead transportation (limbo time), or in deadhead transportation from a duty assignment, to a place of final release; (2) for more than 12 consecutive hours; or (3) unless the employee has had at least 10 consecutive (currently, eight consecutive) hours off duty during the previous 24 hours.

Prohibits requiring or allowing such an employee to remain or go on duty after that employee has initiated an on-duty period each day for: (1) six consecutive days, unless the employee has had at least 48 consecutive hours off duty at the employee's home terminal; or (2) for seven consecutive days, if permitted by a collective bargaining agreement, unless the employee has had at least 72 consecutive hours of duty at a home terminal.

Caps the total number of hours that a train employee may spend in limbo time, or in deadhead transportation from a duty assignment to the place of final release, following a 12-consecutive hour period on duty, that is neither time on duty nor time off duty, unless the train is delayed by an accident, a major equipment failure, or a delay resulting from a cause unknown and unforeseeable to a railroad carrier.

Revises hours of service requirements for signal employees, including signal employees of contractors or subcontractors. Repeals the requirement that a signal employee have at least eight consecutive hours off duty during any 24 hour period. Makes 12 consecutive hours the maximum time on duty, unless the employee has had at least 10 consecutive hours off duty during the previous 24 hours.

Prohibits a signal employee from being allowed to go on duty under certain emergency authority to conduct routine repairs, routine maintenance, or routine inspection of signal systems.

Prohibits a railroad from communicating with a train or signal employee during time off duty, except to notify the employee of an emergency situation.

Prescribes requirements for application of the hours of service regime to commuter and intercity passenger railroad train employees.

Authorizes the Secretary to issue regulations that make certain additional changes to hours of service requirements in order to improve safety and reduce employee fatigue.

Directs the Secretary to conduct at least two pilot projects to analyze specific practices which may be used to reduce fatigue for train, engine, and other railroad employees.

(Sec. 109) Prohibits the Secretary from disclosing to the public any information obtained as part of a railroad's risk reduction program or pilot program, except to enforce or carry out federal law.

Directs the Secretary to: (1) evaluate whether it is in the public interest, including public safety and the legal rights of persons injured in railroad accidents, to withhold from discovery or admission into evidence in a federal or state court proceeding for damages involving personal injury or wrongful death against a carrier any report or data compiled regarding a railroad safety risk reduction program required under this chapter; and (2) implement a rule addressing the results of the evaluation.

(Sec. 110) Authorizes a railroad carrier or railroad carriers, and all nonprofit employee labor organizations representing any class or craft of directly affected covered service employees, to petition the Secretary of Transportation jointly for a waiver of the requirements of this title in order to enable establishment of one or more pilot projects to demonstrate the possible benefits of implementing alternatives to the strict application of such requirements, including those for maximum on-duty and minimum off-duty periods.

Title II: Highway-Rail Grade Crossing and Pedestrian Safety and Trespasser Prevention - (Sec. 201) Requires the Secretary to issue guidance to passenger railroads on methods and strategies to prevent pedestrian accidents, injuries, and fatalities at or near passenger stations.

(Sec. 202) Directs the Secretary to: (1) identify the 10 states that have had the most highway-rail grade crossing collisions, on average, over the past three years; and (2) require them to develop a state grade crossing action plan for the Secretary's approval that identifies specific solutions for improving safety at highway-rail grade crossings, particularly crossings that are at high risk for multiple accidents.

(Sec. 203) Requires the Secretary to develop model legislation for states to improve safety by addressing sight obstructions at highway-rail grade crossings which have only passive warnings.

(Sec. 204) Requires each railroad carrier and each state to report to the Secretary current information about previously unreported highway-rail grade crossings, with annual updates, for a national crossing inventory. Establishes civil penalties for violation of such requirements by a railroad carrier.

(Sec. 205) Replaces the expired pilot demonstration program for emergency notification of grade crossing problems with a permanent system.

Directs the Secretary to require each railroad carrier to: (1) establish a toll-free telephone service to receive directly calls reporting malfunctions of signals, disabled vehicles blocking railroad tracks at grade crossings, obstructions to the view of a train's approach, or other related safety information; (2) warn any trains operating near the grade crossing immediately upon receiving such a report, and contact appropriate public safety officials to direct traffic and remove any disabled vehicle; (3) timely investigate any report of a view obstruction and remove it if possible, or correct any other reported unsafe circumstance; and (4) ensure placement of the toll-free telephone number and certain other explanatory information on signs at each grade crossing. Authorizes the Secretary to waive the requirement that telephone service be toll-free for Class II and Class III rail carriers if such service would be cost prohibitive.

(Sec. 206) Directs the FRA to make grants to Operation Lifesaver to: (1) carry out a public information and education program to help prevent and reduce railroad accidents, incidents, injuries, and fatalities, and to improve awareness along railroad rights-of-way and at highway-rail grade crossings; and (2) implement a pilot Railroad Safety Public Awareness Program addressing the need for targeted and sustained community outreach on rail and grade crossing safety. Authorizes appropriations for FY2010-FY2013.

(Sec. 207) Directs the Secretary to make grants to: (1) up to three states annually to develop or continue public education activities and enforcement of highway-rail crossing safety laws; and (2) provide for priority highway-rail grade crossing safety improvements. Authorizes appropriations for FY2010-FY2013.

(Sec. 208) Directs the Secretary to: (1) review current local, state, and federal laws regarding trespassing and vandalism on railroad property and violations of highway-rail grade crossing warning signs; and (2) develop and make available to state and local governments model state legislation providing for civil or criminal penalties, or both, for violations of highway-rail grade crossing warning signs.

Authorizes the Secretary to purchase items of nominal value and distribute them to the public without charge as part of an educational or awareness program to improve the safety of highway-rail crossings and prevent trespass on railroad rights-of-way.

(Sec. 209) Requires the FRA to conduct periodic audits of each Class I railroad and non-Class I railroad to ensure that all grade crossing collisions and fatalities are reported to the national accident database.

(Sec. 210) Authorizes railroad carriers and railroad suppliers to submit for the Secretary's approval new technology providing warning to highway users at highway-rail grade crossings. Declares that such Secretarial approval preempts state law concerning the adequacy of such technology.

Title III: Federal Railroad Administration - (Sec. 301) Requires the Secretary to gradually increase the number of rail safety-related employees at the FRA by 200 between FY2009-FY2013.

(Sec. 302) Increases penalties for violations of rail safety regulations prescribed or orders issued by the Secretary, including violations related to rail accident reporting and hours-of-service.

(Sec. 303) Requires the Secretary to make publicly available, and publish on the FRA public website, an annual report of all railroad enforcement actions taken by the Secretary or the FRA during the prior fiscal year.

(Sec. 305) Revises the Secretary's authority to prohibit an individual from performing safety-sensitive functions in the railroad industry because of previous violations of hazardous materials transportation laws.

(Sec. 306) Allows the Secretary to authorize officers, employees, or agents to intercept and record a radio communication, with or without the consent of the sender or other receivers of the communication, where such communication is broadcast or transmitted over a radio frequency authorized for use by one or more railroad carriers by the Federal Communications Commission (FCC) and primarily used by such railroad carriers for communications in connection with railroad operations. Allows such activities for purposes of accident prevention and accident investigation. Sets forth uses of information obtained through such activities.

(Sec. 307) Requires the Secretary to update the FRA website to: (1) help the public find current information regarding FRA activities; and (2) provide a mechanism for the public to report to the FRA potential violations of federal railroad safety and hazardous materials transportation laws and orders.

(Sec. 308)Authorizes the Secretary in emergency situations to waive compliance with a railroad safety order without prior notice and comment provided certain conditions are met.

Title IV: Railroad Safety Enhancements - (Sec. 401) Directs the Secretary to establish: (1) minimum training standards for each class and craft of safety-related railroad employees and railroad carrier contractor and subcontractor employees to become knowledgeable with federal railroad safety laws and regulations and railroad carrier rules and procedures to implement such laws and regulations; (2) a requirement that railroad carriers, contractors, and subcontractors develop and submit for the Secretary's approval employee training and qualification plans; and (3) minimum training curriculum to ensure safety-related railroad employees and contractor and subcontractor employees are qualified to identify and correct defective conditions that could lead to rail accidents or injuries.

(Sec. 402) Directs the Secretary to: (1) establish a program to require the certification of train conductors; and (2) report to specified congressional committees about whether the certification of certain crafts or classes of railroad carrier or railroad carrier contractor or subcontractor employees is necessary to reduce the number and rate of railroad accidents or to improve railroad safety.

(Sec. 403) Requires the Secretary to: (1) report to specified congressional committees on a study of whether the required intervals of track inspections for each class of track and track remedial action requirements should be amended, whether different track inspection and repair priorities or methods should be required, and whether the speed at which railroad track inspection vehicles operate and the scope of territory they cover allow for proper track inspection, as well as whether such speed and scope should be regulated by the Secretary; and (2) issue regulations for concrete cross ties for class one through five track.

(Sec. 404) Requires the Secretary to study methods to improve the safety of rail passenger station platform gaps to comply with the Americans with Disabilities Act, and to minimize the associated safety risks of such gaps for railroad passengers and employees.

(Sec. 405) Directs the Secretary to study and report to specified congressional committees on the safety impact of the use of personal electronic devices, including cell phones, video games, and other distracting devices, by safety-related railroad employees during work. Authorizes the Secretary to study other elements of the locomotive cab environment and their effect on an employee's health and safety.

Authorizes the Secretary, based on the conclusions of the studies, to: (1) prohibit the use of such devices during work, unless they are being used in accordance with railroad operating rules; and (2) issue regulations to improve elements of the cab environment to protect an employee's health and safety.

(Sec. 406) Requires the Secretary to issue standards governing the development and use of rail safety technology in dark territory (any territory in a railroad system that does not have a signal or train control system installed or operational).

(Sec. 407) Authorizes the Secretary, upon petition by a group of commonly controlled railroad carriers operating within the United States as a single, integrated rail system, to treat such group as a single railroad carrier for railroad safety purposes.

(Sec. 408) Requires the Secretary to study and report to Congress on the impacts of repealing a provision of the Regional Rail Reorganization Act of 1973 which preempts state laws from requiring certain crew requirements in the former region of the Consolidated Rail Corporation (Conrail).

(Sec. 409) Requires any nonfederal alcohol and drug testing program of a railroad carrier to provide that all post-employment tests of the specimens of employees performed under the program be conducted using a scientifically recognized method of testing capable of determining the presence of the specific analyte at a level above the cutoff level established by the carrier.

Requires each railroad carrier that has such a testing program to provide a redress process for its employees who were determined to be in violation of the program.

(Sec. 410) Directs the Secretary to require each Class I railroad, and any other railroad that the Secretary determines appropriate, to: (1) develop, and submit for the Secretary's approval, a critical incident stress plan that provides for debriefing, counseling, guidance, and other appropriate support services to be offered to an employee affected by a critical incident; (2) allow for the immediate relief from duty of any employee involved in a critical incident; (3) relieve a requesting employee who witnessed a critical incident of his or her duties as soon as feasible.

(Sec. 411) Requires the Secretary to study and report to Congress on the potential hazards to which railroad carrier employees and railroad contractors or subcontractors are exposed during the transportation of high-level radioactive waste and spent nuclear fuel.

(Sec. 413) Directs the Secretary to issue regulations to require railroad carriers to: (1) provide emergency escape breathing apparatus for all crewmembers in locomotive cabs on freight trains carrying hazardous materials; and (2) provide their crewmembers with training in the use of such apparatus.

(Sec. 414) Requires each railroad carrier to document, for at least two years, certain historical information on its tunnels, including inspection and maintenance activities.

(Sec. 415) Requires the Secretary to study, and report to Congress on, safety inspection requirements for diesel-electric locomotives and equipment operated by railroad-related museums, historical societies, and tourist or scenic railroads, as well as an analysis of the safety consequences of requiring less frequent inspections of such locomotives and equipment.

(Sec. 416) Prohibits mechanical and brake inspections of rail cars performed in Mexico from satisfying U.S. rail safety laws and regulations unless the Secretary certifies that: (1) such inspections are being performed under regulations and standards equivalent to those applicable in the United States; (2) the inspections are being performed by employees that have received training similar to training received by U.S. railroad employees; (3) inspection records are required to be available to the crewmembers aboard the train; and (4) the FRA is permitted to perform onsite inspections to ensure compliance with the requirements of this section.

(Sec. 419) Revises employee protection requirements to prohibit a railroad carrier or other covered person from: (1) denying or interfering with the medical or first aid treatment of a railroad employee injured during the course of employment; or (2) disciplining or threatening to discipline a railroad employee who requests such treatment.

(Sec. 420) Revises rail employee sleeping quarters requirements to require a railroad carrier that provides sleeping quarters for its employees to provide indoor toilet facilities, potable water, and other features to protect their health. Requires camp car compliance with such requirement by December 31, 2010.

Title V: Rail Passenger Disaster Family Assistance - (Sec. 501) Directs the NTSB, as soon as practicable after being notified of a rail passenger accident resulting in major loss of life, to provide certain assistance to families of passengers involved in the accident.

(Sec. 502) Requires a rail passenger carrier to submit to the NTSB, the Secretary, and the Secretary of Homeland Security a plan for addressing the needs of families of passengers involved in an accident of a rail passenger carrier intercity train resulting in major loss of life. Provides for FY2010 funding.

(Sec. 503) Requires the Secretary to establish a task force to develop a model plan and recommendations on how passenger rail carriers can provide assistance and notification to families of passengers involved in rail accidents.

Title VI: Clarification of Federal Jurisdiction Over Solid Waste Facilities - Clean Railroads Act of 2008 - (Sec. 602) Exempts solid waste rail transfer facilities from the jurisdiction of the Surface Transportation Board (effectively allowing state and local authorities to regulate such facilities).

Declares that any such facility lacking a state permit shall not be required to possess one (other than a siting permit): (1) if by a certain deadline the facility has applied, in good faith, for all required permits; and (2) until the permitting agency has either approved or denied the permit application.

Declares that any such facility that does not possess a state siting permit shall not be required to possess one to continue to operate or to comply with state land use requirements. Authorizes a state governor to petition the Surface Transportation Board to require the facility to apply for a land-use exemption. Requires the Board to accept such a petition and the facility to have such an exception to continue to operate.

Authorizes the Administrator of the Environmental Protection Agency (EPA) to make modifications to such requirements to protect human health and the environment.

(Sec. 604) Authorizes the Board to issue a land-use exemption for a solid waste rail transfer facility operated or proposed to be operated by or on behalf of a rail carrier if: (1) state or local law affecting the siting unreasonably burdens the interstate railroad transportation of solid waste, or discriminates against such transportation and a solid waste rail transfer facility, or a rail carrier that owns or operates such a facility petitions the Board for such an exemption; or (2) the governor (or designee) of a state in which a facility that is already operating is located petitions the Board to initiate a permit proceeding for that particular facility.

Allows the Board to issue a land use exemption only if the facility at the existing or proposed location does not pose an unreasonable risk to public health, safety, or the environment. Prohibits any such land-use exemption for a solid waste rail transfer facility proposed to be located on land within the National Park System, the National Wildlife Refuge System, the National Wilderness Preservation System, the National Trails System, the National Wild and Scenic Rivers System, a National Reserve, a National Monument, or certain lands for which a state has implemented a conservation management plan, if the facility's operation would be inconsistent with restrictions placed on such land.

Title VII: Technical Corrections - (Sec. 701) Makes technical corrections to limitations on the use of local rail freight assistance. Considers any repaid portion of the U.S. Government's share of money, and any contingent interest recovered, to be state funds.

Redefines "motor carrier" to exempt from unified carrier registration system plan and agreement requirements any carrier that the board of directors of the unified carrier registration plan determines appropriate.

Amends the Railroad Revitalization and Regulatory Reform Act of 1976 to extend from 25 years to 35 years the repayment term of direct loans or loan guarantees for improvement of intermodal or rail equipment or facility projects.

(Sec. 201) Defines the national rail passenger transportation system as: (1) Amtrak's Boston-Washington Northeast Corridor; (2) high-speed corridors designated by the Secretary once regularly scheduled intercity service over them has been established; (3) long-distance routes (of greater than 750 miles) operated on the date of enactment of this Act; and (4) short-distance routes operated by Amtrak or a non-Amtrak recipient of federal capital assistance.

Authorizes Amtrak and a state to agree on the operation of an intercity route or service not included in the national rail transportation system.

Declares that this Act does not preclude Amtrak from restoring, improving, or developing non-high-speed intercity passenger rail service.

Provides that: (1) the mission of Amtrak is to provide efficient and effective intercity passenger rail mobility consisting of high quality service that is trip-time competitive with other intercity travel options and that is consistent with certain goals; and (2) one of Amtrak's goals shall be to provide additional or complimentary intercity transportation service to ensure mobility in a natural disaster or other times where travel options are not adequately available.

(Sec. 203) Authorizes the Amtrak Board of Directors to employ an independent financial consultant with experience in railroad accounting to assist Amtrak in improving Amtrak's financial accounting and reporting system and practices.

Requires the Amtrak Board to: (1) implement a modern financial accounting and reporting system not later than three years after enactment of this Act; and (2) develop a five-year financial plan.

(Sec. 205) Authorizes the Secretary of the Treasury to make agreements to restructure Amtrak's long-term debt and capital leases.

(Sec. 206) Directs the Secretary of Transportation to establish substantive and procedural requirements for grant requests, including a 30-day approval process.

(Sec. 207) Requires the FRA and Amtrak to develop jointly new or improve existing metrics and minimum standards for measuring the performance and service quality of intercity passenger train operations.

(Sec. 208) Directs the FRA to obtain the services of an independent entity to develop and recommend objective methodologies for Amtrak intercity passenger routes and services.

(Sec. 209) Directs the Amtrak Board to develop and implement a single methodology for allocating train route operating and capital costs among states and Amtrak.

(Sec. 210) Requires Amtrak to evaluate the financial and operating performance of long distance passenger rail routes, rank them, and develop and post on its website a performance improvement plan.

Requires Amtrak and the Rhode Island Department of Transportation (RIDOT) to agree by July 1, 2009, on access fees and other charges to be charged for RIDOT's operation of the South County commuter rail service on the Northeast Corridor between Providence and Wickford Junction, Rhode Island.

Directs Amtrak to report to Congress on infrastructure and equipment improvements necessary to provide regular high-speed service within specified periods of time between Washington, D.C. and New York City and between New York City and Boston. Requires the Northeast Corridor Infrastructure and Operations Advisory Commission to report to Congress on the role of Amtrak's Northeast Corridor service in the economic development of the Northeast Corridor.

(Sec. 213) Authorizes the Surface Transportation Board (STB) to: (1) investigate the causes of any passenger train performance of under 80% for any two consecutive calendar quarters; (2) determine if delays or failure to achieve minimum standards can be attributed to a rail carrier's failure to prefer Amtrak over freight transportation; and (3) assess damages upon a host rail carrier for such delays or failures. Allows Amtrak, an intercity passenger rail operator, freight railroads that host Amtrak trains, or an entity (state) for which Amtrak operates intercity passenger rail service to petition the STB directly for an investigation of such delays or failures. Authorizes the STB to: (1) establish and collect fees from any entity that files a complaint or otherwise requests its services; and (2) increase the number of its employees by up to 15 for the five fiscal year period beginning with FY2009.

(Sec. 214) Directs the FRA to establish an alternative passenger rail service program that allows a rail carrier or carriers that own a route over which Amtrak operates to petition FRA to become a passenger rail carrier for that route in lieu of Amtrak for a period of up to five years.

(Sec. 215) Directs the Secretary to develop an employee transition assistance program for Amtrak employees adversely affected by the cessation of a long distance or any other route previously operated by Amtrak. Authorizes appropriations.

(Sec. 216) Encourages Amtrak to increase the operation of special trains funded by private sector operators through competitive contracting to minimize the need for federal subsidies.

(Sec. 217) Permits a state to make an agreement with Amtrak to use facilities and equipment of, or have services provided by, Amtrak to enable the state to utilize an entity other than Amtrak to provide services required for operation of the route.

(Sec. 219) Directs Amtrak to evaluate improvements necessary to make all existing intercity rail stations readily accessible to and usable by individuals with disabilities. Authorizes appropriations.

(Sec. 220) Directs the FRA to monitor and conduct periodic reviews of Amtrak's compliance with the Americans with Disabilities Act of 1990 (ADA) and the Rehabilitation Act of 1974 to ensure Amtrak's services and facilities are accessible to individuals with disabilities.

(Sec. 221) Directs the Inspector General of DOT to assess progress made by Amtrak management and the DOT in implementing this Act.

Directs the Secretary to: (1) analyze the December 1, 1998, extension of the designation of the Southeast High-Speed Rail Corridor, including the feasibility of expanding the Keystone Corridor to Cleveland, Ohio, and the South Central High-Speed Rail Corridor to the Port of Houston, Texas, to Memphis, Tennessee, and south of San Antonio to a location in far south Texas to be chosen at the discretion of the Secretary; and (2) establish a process for a state or group of states to petition the Secretary to redesignate or modify any designated high-speed rail corridors.

(Sec. 225) Requires the Inspector General of the DOT to report to Congress on service delays on the Coast Starlight (between Seattle, Washington, and Los Angeles, California) and the Amtrak Cascades (between Vancouver, British Columbia, Canada, and Eugene, Oregon) rail routes and recommendations for improving the on-time performance of such routes.

(Sec. 226) Requires Amtrak to submit to Congress a plan for restoring passenger rail service between New Orleans, Louisiana, and Sanford, Florida.

(Sec. 227) Directs the Inspector General of the DOT to report to Congress on Amtrak's utilization of its equipment maintenance and repair facilities, including the Beech Grove Mechanical Facility in Indiana.

(Sec. 228) Expresses the sense of Congress that Amtrak should maintain a national passenger rail system that connects the continental United States from coast to coast and from border to border.

Title III: Intercity Passenger Rail Policy - (Sec. 301) Authorizes the Secretary to make grants to an applicant state, group of states, Interstate Compact, or public agency to assist in financing the capital costs of facilities, infrastructure, and equipment necessary to provide intercity passenger rail transportation. Authorizes appropriations for FY2009-FY2013.

(Sec. 302) Authorizes the Secretary to make congestion grants to states, or to Amtrak in cooperation with states, for the capital costs of facilities and equipment for high priority rail corridor projects necessary to reduce congestion or facilitate ridership growth in intercity passenger rail transportation. Authorizes appropriations for FY2010-FY2013.

(Sec. 303) Authorizes states to prepare and maintain a state rail plan that: (1) sets forth state policy involving freight and passenger rail transportation (including commuter rail operations); and (2) includes a long-range rail investment program. Requires the Secretary to prescribe procedures for the review of state rail plans.

(Sec. 304) Requires the FRA, working with Amtrak, the STB, the city of Baltimore, the state of Maryland, and non-Amtrak rail operators to: (1) approve a new rail tunnel alignment in Baltimore that will allow an increase in train speed and service reliability; and (2) ensure completion of the related environmental review process. Authorizes appropriations for FY2009-FY2013.

(Sec. 306) Directs the Secretary to establish a rail cooperative research program to address intercity rail passenger and freight rail services, including ways to expand the transportation of international trade traffic, enhance the efficiency of intermodal interchange at ports and other intermodal terminals, and increase availability of rail service for seasonal freight needs. Directs the Secretary to establish an advisory board to recommend research, technology, and technology transfer activities related to rail passenger and freight transportation. Authorizes appropriations for FY2010-FY2013.

(Sec. 307) Sets forth additional duties of the FRA Administrator, including to provide assistance to states in developing state rail plans, and to develop a long-range national rail plan. Requires the Administrator to develop a schedule for achieving specific, measurable performance goals.

Title IV: Miscellaneous - (Sec. 401) Authorizes a public transportation authority or rail carrier to submit disputes over trackage use and railroad rights-of-way to the STB for nonbinding mediation.

(Sec. 402) Encourages Amtrak, commuter rail entities, regional and state public transportation authorities, and freight railroad carriers to engage in good faith discussions with respect to the routing and timing of trains to efficiently move, particularly during peak hours, the maximum number of commuter, intercity, and passenger rail passengers.

(Sec. 403) Expresses the sense of Congress that: (1) expanded commuter rail service between New Haven, Connecticut, and Springfield, Massachusetts, is an important transportation priority; and (2) Amtrak should work cooperatively with the states of Connecticut and Massachusetts to enable such expanded service.

(Sec. 404) Directs the Secretary to study and report to Congress on: (1) the extent to which freight railroads, Amtrak, and other passenger rail operators could use biofuel blends to power locomotives and other vehicles that can operate on diesel fuel; and (2) the feasibility of using biodegradable lubricants for freight and passenger railroad locomotives, rolling stock, or their equipment.

(Sec. 406) Requires Amtrak to develop a strategic plan on expanded cross-border passenger rail (Amtrak Cascades) service between the United States and Canada during the 2010 Olympic Games.

Authorizes the Secretary and other federal agencies to establish facilities and procedures to conduct preclearance of passengers on Amtrak trains entering the United States from Canada.

(Sec. 407) Directs the Secretary to: (1) find ways to streamline compliance with specified National Historic Preservation Act requirements for federally-funded railroad infrastructure repair and improvement projects; and (2) take immediate action to cooperate with named Alaska and North Carolina entities in expediting the decisionmaking process for safety-related projects involving railroad and Southeast High Speed Rail Corridor property and facilities that have disputed historic significance.

Directs the Secretary to establish a high-speed rail corridor development program. Authorizes the Secretary to make competitive grants to a state, a group of states, an Interstate Compact, a public agency, or Amtrak to finance capital projects in high-speed rail corridors. Authorizes appropriations for FY2009-FY2013.

(Sec. 502) Directs the Secretary to solicit proposals for projects for operation of a high-speed intercity passenger rail system within specified high-speed rail corridors.

Title VI: Capital and Preventive Maintenance Projects for Washington Metropolitan Area Transit Authority - (Sec. 601) Authorizes the Secretary to make grants to the Washington Metropolitan Area Transit Authority (WMATA, or Metro) to finance in part the capital and preventive maintenance projects included in its Capital Improvement Program. Conditions the availability of funds, in part, on assurance that each licensed wireless provider serving the public within the rail system has access to the system on an ongoing basis.